jonas

Hi all, you can download the phastcons elements for mouse here: https://genome.ucsc.edu/cgi-bin/hgTables ("35 Vert El."). If you read the downloaded bed file into R and convert it to [GRanges](https://bioconductor.org/packages/devel/bioc/vignettes/GenomicRanges/inst/doc/GenomicRangesIntroduction.html), Pando...

Hi @bjstewart1, currently Pando would expect log-normalized data (for RNA) and tf-idf-normalized data (for ATAC) as input and would also generally use that by default if it's in the `data`...

It's possible that this is because the graph is disconnected and certain nodes cannot be reached from a TF. I'll see if I can fix this to through a warning...

The function `NetworkTFs()` should return a sparse matrix with TFs a colnames, if this is not the case there is a chance something went wrong earlier in the workflow. What...

As you noticed @jsacco1, Pando is unfortunately not compatible with recent versions of SeuratObject. I'm not sure how much time I will have to fix this in the near future,...

- `estimate` is essentially the coefficient of the linear model that is fit by pando. It should indicate the strength and direction of the regulatory interaction. - `correlation` indicated the...

Hi @AmelZulji, when doing case-control comparisons we've usually run Pando on both conditions together and then tested for differential module activity or reg region accessibility. I personally would probably not...

Hi @AmelZulji, yes, that `AddModuleScore()` is definitely one way to do this. You could then test for diff activity very simply with a t-test/ANOVA. Since you have replicates, I would...

Yes, this is true for the umap layout, since here genes are represented by their regulators in the GRN. If you use another (e.g. forece-directed) layout for the GRN then...

I'm not fully sure what the problem here is. Maybe you can check if the TFs you want are indeed in the module graph computed by Pando. It's possible that...